US 10,854,315 B2 · Systems and methods for determining structural variation and phasing using variant call data

Abstract

Systems and methods for determining structural variation and phasing using variant call data obtained from nucleic acid of a biological sample are provided. Sequence reads are obtained, each comprising a portion corresponding to a subset of the test nucleic acid and a portion encoding a barcode independent of the sequencing data. Bin information is obtained. Each bin represents a different portion of the sample nucleic acid. Each bin corresponds to a set of sequence reads in a plurality of sets of sequence reads formed from the sequence reads such that each sequence read in a respective set of sequence reads corresponds to a subset of the nucleic acid represented by the bin corresponding to the respective set. Binomial tests identify bin pairs having more sequence reads with the same barcode in common than expected by chance. Probabilistic models determine structural variation likelihood from the sequence reads of these bin pairs.

A method of phasing sequencing data of a test nucleic acid sample obtained from a biological sample from a single organism of a species, wherein the test nucleic acid sample comprises a first set of haplotypes (H0) and a second set of haplotypes (H1), the method comprising:

at a computer system having one or more processors, and memory storing one or more programs for execution by the one or more processors:
(A) obtaining a reference sequence for all or a portion of a genome of the species;
(B) obtaining a plurality of variant calls Ai;p for the biological sample, wherein
i is an index to a position in the reference sequence, and
p∈{0, 1, −1} in which label 0 assigns a respective variant call in Ai;p to HO, label 1 assigns the respective variant call to H1, and label −1 assigns the respective variant call to the zygosity error condition H−1;
(C) obtaining a plurality of sequence reads {right arrow over (O)} for the biological sample, wherein
the plurality of sequence reads {right arrow over (O)} comprises at least 100,000 sequence reads and collectively represents at least 1000 different regions of the reference sequence,
each respective sequence read {right arrow over (O)}i in the plurality of sequence reads comprises a first portion that corresponds to a subset of the reference sequence and a second portion that encodes a respective barcode, independent of the reference sequence, for the respective sequence read, in a plurality of barcodes, and
each respective sequence read {right arrow over (O)}i in the plurality of sequence reads is ∈{0, 1, −1, −}n, wherein (i) n is the number of variants calls in Ai;p, (ii) each respective label 0 for the respective sequence read {right arrow over (O)}i assigns a corresponding variant call in Ai;p to H0, (iii) each respective label 1 for the respective sequence read {right arrow over (O)}i assigns a corresponding variant call in Ai;p to H1, (iv) each respective label −1 for the respective sequence read {right arrow over (O)}i assigns a corresponding variant call in Ai;p to H−1, and (v) each respective label − for the respective sequence read {right arrow over (O)}i indicates that the corresponding variant call in Ai;p is not covered;
and
(D) refining a phasing vector result {right arrow over (X)} by optimization of haplotype assignments at individual positions i in Ai;p between HO, H1 and H−1 for the plurality of sequence reads using an overall objective function:
X
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εi is an estimate of incurring H−1 at position i,
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{circumflex over (X)} is the refined phasing vector result,
C is a constant,
{right arrow over (X)} is the phasing vector result to be inferred, and
(O1,f, . . . , ON,f) is the respective subset of N variant calls in the plurality of variant calls Ai;p observed in the subset of sequence reads that include the same respective barcode from the plurality of barcodes,
thereby phasing sequencing data of the test nucleic acid sample in the form of the refined phasing vector result {right arrow over (X)}.

130 more elements

Facts

Application

15/019,928Filed 9 Feb 2016 · continuation

Priority

9 Feb 2015

Published

US 2016/0232291 A111 Aug 2016

Granted

1 Dec 2020

Term ends

Not estimatedThe source records don’t support an estimate.

Classification11 codes

C12Q 1/6837
Enzymatic or biochemical coupling of nucleic acids to a solid phase: using probe arrays or probe chips
G16B 20/20
ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations: allele or variant detection, e.g. single…
A61P 3/00
Drugs for disorders of the metabolism
A61P 43/00
Drugs for specific purposes, not provided for in groups a61p1/00-a61p41/00

Family

Application62/113,693Us provisional application · filed 9 Feb 2015

Application62/120,247Us provisional application · filed 24 Feb 2015

Application62/120,330Us provisional application · filed 24 Feb 2015

Application62/238,077Us provisional application · filed 6 Oct 2015

PCT/US2016/017196Parent of this continuation · filed 9 Feb 2016

US 2016/0232291 A1Pre-grant publication · published 11 Aug 2016

US 10,854,315 B2This patent

From the US filing history. Foreign family members aren’t listed.

Systems and methods for determining structural variation and phasing using variant call data

Life of this patent

Systems and methods for determining structural variation and phasing using variant call data

Life of this patent

Abstract

Claims30